The principle of the GeneRead DNAseq V2 System is to employ overlapping primer sets across the exonic portions of a gene or genes to maximize target coverage and minimize nonspecific amplification.

Performance

The performance of GeneRead DNAseq Targeted Panels V2 is assessed by 3 criteria: design coverage, specificity, and coverage uniformity. Greater than 95% of exonic regions are covered by the panel primer design, enhancing potential variant discovery. The high specificity of the system maximizes efficient use of sequencing capacity, as more than 95% of sequencing reads align to target regions. Finally, the high coverage uniformity of the system, with more than 90% of targeted bases covered at >20% median sequencing depth, ensures high-quality variant calls.

Outstanding experimental performance metrics

Type

Panel name

Coverage (%)

Specificity (%)

Uniformity (%)

Solid tumors

Tumor Actionable Mutations

100.0

98.2

91

Clinically Relevant Tumor

98.1

95.3

90

Hematologic malignancies

Myeloid Neoplasms

98.1

97.4

94

Disease-specific

Breast Cancer

98.2

96.8

91

Colorectal Cancer

98.7

98.3

95

Liver Cancer

99.0

96.4

96

Lung Cancer

97.5

98.1

90

Ovarian Cancer

98.9

96.6

96

Prostate Cancer

98.4

97.3

94

Gastric Cancer

98.1

98.5

93

Cardiomyopathy

96.3

96.7

87

Comprehensive

Carrier Testing

97.5

97.9

91

Cancer Predisposition

98.3

96.8

93

Comprehensive Cancer

98.0

97.7

92

Gene-specific

BRCA1 and BRCA2

100.0

99.0

97

Principle

The GeneRead DNAseq Targeted Panel System employs overlapping primer sets across the exonic portions of a gene or group of genes to maximize target coverage (see Multiplex PCR-enabled target enrichment of genomic regions of interest). Overlapping primer sets are divided into an appropriate number of pools to maximize specificity. Following amplification and purification, enriched regions from each sample are pooled together, yielding one library preparation for each sample.

Specifications of GeneRead DNAseq Targeted Panels V2

Type

Panel name

# Genes

# Amplicons

Target region (bases)

Solid tumors

Tumor Actionable Mutations

8

118

7104

Clinically Relevant Tumor

24

602

39603

Hematologic malignancy

Myeloid Neoplasms

50

2536

236319

Disease-specific

Breast Cancer

44

2915

268621

Colorectal Cancer

38

1954

182851

Liver Cancer

33

2052

191170

Lung Cancer

45

3586

332999

Ovarian Cancer

32

2021

198058

Prostate Cancer

32

1837

167195

Gastric Cancer

29

2377

222333

Cardiomyopathy

58

2657

249727

Comprehensive

Carrier Testing

157

6943

664735

Cancer Predisposition

143

6582

620318

Comprehensive Cancer

160

7951

744835

Gene-specific

BRCA1 and BRCA2

2

250

21472

Procedure

GeneRead DNAseq Targeted Panels V2 are part of a total workflow for targeted next-generation sequencing (see GeneRead DNAseq Targeted Panels V2 workflow). Simply extract DNA from your samples (the QIAamp DNA Mini Kit, the QIAamp DNA FFPE Tissue Kit or the GeneRead DNA FFPE Kit are recommended), quantify and qualify your DNA sample with the GeneRead DNA QuantiMIZE system, and then use the GeneRead DNAseq Targeted Panels V2 in combination with GeneRead DNAseq Panel PCR Kit V2 to perform targeted enrichment using multiplex PCR. Once targets have been enriched, construct the NGS library and use the GeneRead DNAseq Library Quant Array to quantify and perform quality control. Perform NGS. Multiple samples can be analyzed with a single NGS run. Use the Multiplexing Capacity Calculator (see the Resources tab) to determine the optimal number of samples and coverage depth for each NGS run. Analyze your data using the QIAGEN NGS Data Analysis Web Portal or CLC Bio pipelines, and interpret detected variants using the Ingenuity Variant Analysis platform.